LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

comm_modify vel yes
read_data data.swm4-ndp
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     3 = max # of 1-3 neighbors
     3 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
System init for delete_bonds ...
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21745695
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.19728846
  estimated relative force accuracy = 0.00059412835
  using double precision FFTW3
  3d grid and FFT values/proc = 1500 250
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Deleting bonds ...
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
Fix rigid/nph/small setup ...
  create bodies CPU = 0.000 seconds
  500 rigid bodies with 2000 atoms
  0.83209864 = max distance from body owner to body atom
fix NVE DRUDES nve

compute TEMP all temp/drude

thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21745695
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.19728846
  estimated relative force accuracy = 0.00059412835
  using double precision FFTW3
  3d grid and FFT values/proc = 1500 250
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 19.79 | 19.8 | 19.8 Mbytes
   Step         TotEng         KinEng         PotEng         E_bond        E_angle         E_vdwl         E_coul         E_long         Press          Volume          Temp        c_TEMP[1]      c_TEMP[2]   
         0   4568.0413      903.41148      3664.6298      623.46454      0              2890.2449      157955.66     -157804.74      244591.07      13824          202.18534      295.64644      14.858785    
        20   2915.1398      4579.5567     -1664.4168      561.94269      0              600.76832      155095.11     -157922.24      27379.687      14058.573      1024.9142      1455.9144      160.864      
        40   1328.5416      3339.5175     -2010.9759      723.65556      0              584.70467      154597.11     -157916.45      18319.948      14485.678      747.39087      1101.889       36.964165    
        60   326.64132      2728.3035     -2401.6622      577.26208      0              386.89644      154565.05     -157930.87      11759.81       15031.531      610.59993      906.02229      18.537884    
        80  -399.19801      2197.7856     -2596.9836      553.47853      0              277.29748      154509.77     -157937.53      6941.7088      15651.608      491.86893      733.42143      7.7801893    
       100  -905.16383      1883.2744     -2788.4382      543.75184      0              152.04689      154451.95     -157936.19      2721.7257      16300.639      421.48067      629.59532      4.4083994    
       120  -1263.6541      1607.8881     -2871.5422      528.88685      0              43.424721      154493.85     -157937.7      -174.33048      16938.519      359.84867      538.07471      2.6768767    
       140  -1501.2328      1484.663      -2985.8958      537.77049      0             -11.198203      154422        -157934.47     -2188.8769      17540.728      332.27064      497.00403      2.1393169    
       160  -1667.7592      1389.628      -3057.3872      537.7827       0             -25.095705      154371.01     -157941.08     -3110.4894      18093.892      311.0016       465.13217      2.1184351    
       180  -1775.5587      1305.6603     -3081.219       563.07532      0             -1.1076504      154295.63     -157938.81     -3591.9849      18593.474      292.20945      437.12062      1.8076698    
       200  -1902.5566      1209.0189     -3111.5755      578.60952      0              28.037078      154220.53     -157938.75     -3791.0282      19039.305      270.58092      404.7438       1.7139894    
       220  -1980.9904      1202.364      -3183.3544      598.39667      0              53.237275      154104.01     -157939        -4178.2404      19430.909      269.09153      402.47844      1.7845759    
       240  -2064.4281      1151.3269     -3215.755       614.20473      0              112.96281      153995.9      -157938.82     -3825.1976      19765.827      257.66932      385.35391      1.7811825    
       260  -2172.8663      1109.6386     -3282.5049      656.80834      0              166.9647       153832.85     -157939.13     -3818.2201      20048.19       248.33939      371.42983      1.6529201    
       280  -2275.7519      1025.502      -3301.2538      672.58937      0              186.53428      153779.27     -157939.64     -4001.8817      20279.116      229.50944      343.18239      1.7013517    
       300  -2317.3517      1045.1479     -3362.4996      698.78467      0              210.90443      153666.43     -157938.62     -3851.4445      20458.033      233.90625      349.85269      1.5430293    
       320  -2367.8047      1075.9304     -3443.7351      707.66032      0              227.0194       153561.72     -157940.14     -3985.1408      20586.294      240.79544      360.09195      1.7118475    
       340  -2426.4705      1056.9        -3483.3705      742.56768      0              285.75697      153428.3      -157939.99     -3760.4689      20664.378      236.5364       353.7014       1.733189     
       360  -2469.348       1043.5025     -3512.8505      767.40945      0              308.67039      153351.63     -157940.56     -3804.1035      20695.388      233.53801      349.24732      1.6492193    
       380  -2539.5276      1038.7991     -3578.3267      794.67751      0              352.43563      153212.97     -157938.41     -3456.0244      20681.199      232.48537      347.63249      1.7322499    
       400  -2588.8296      1032.5299     -3621.3595      827.52183      0              412.02318      153080.63     -157941.54     -3244.0723      20624.525      231.08231      345.56181      1.6727014    
       420  -2652.5511      982.61434     -3635.1654      854.36803      0              453.46737      153000.23     -157943.23     -2636.3227      20530.357      219.91111      328.74939      1.7888047    
       440  -2701.7132      975.8062      -3677.5194      892.15092      0              498.31751      152870.74     -157938.73     -2711.3191      20404.46       218.38743      326.51291      1.6942347    
       460  -2739.979       1011.5229     -3751.5019      927.23053      0              531.61712      152731.16     -157941.51     -2707.6034      20249.834      226.38091      338.47646      1.7517192    
       480  -2780.935       998.74744     -3779.6824      939.37874      0              549.29055      152674.99     -157943.34     -2456.1094      20069.043      223.52173      334.19567      1.7184901    
       500  -2831.4674      985.86278     -3817.3302      966.82215      0              594.07318      152562.52     -157940.74     -2076.2404      19865.016      220.63811      329.8698       1.7330794    
       520  -2887.5954      1020.0793     -3907.6747      1008.4623      0              624.86225      152399.27     -157940.27     -2084.7168      19642.675      228.29583      341.34532      1.7412513    
       540  -2948.3607      1000.5254     -3948.8861      1028.3338      0              657.6201       152305.7      -157940.54     -2018.1765      19404.393      223.91964      334.76402      1.7638139    
       560  -3006.2195      996.47453     -4002.6941      1059.1313      0              714.08433      152165.03     -157940.94     -1307.971       19154.078      223.01305      333.4261       1.7684588    
       580  -3049.3976      978.27507     -4027.6727      1097.1867      0              793.48986      152019.62     -157937.97     -411.49254      18898.213      218.93997      327.23474      1.9100159    
       600  -3055.3519      980.06883     -4035.4208      1144.1767      0              821.11758      151940.95     -157941.67     -341.12013      18645.262      219.34141      327.79673      1.9895888    
       620  -3070.3872      1001.4302     -4071.8174      1151.1834      0              815.28388      151902.76     -157941.04     -375.56412      18399.655      224.12213      335.05368      1.8203693    
       640  -3095.2132      992.32959     -4087.5428      1139.8666      0              813.85925      151900.17     -157941.44      35.566627      18161.046      222.0854       331.97475      1.8604534    
       660  -3179.6738      969.11302     -4148.7869      1192.9221      0              877.18994      151723.57     -157942.47      381.0437       17929.559      216.88948      324.15805      1.9303013    
       680  -3208.1962      999.08835     -4207.2845      1250.1042      0              907.92806      151576.18     -157941.5       70.259175      17708.098      223.59802      334.24324      1.8645432    
       700  -3229.7965      1019.7044     -4249.5009      1258.0941      0              912.56107      151522.26     -157942.42      215.81282      17496.717      228.21193      341.17159      1.8423187    
       720  -3264.6276      1024.4595     -4289.0871      1260.59        0              911.87938      151482.74     -157944.3       189.48099      17295.66       229.27614      342.70753      1.9418623    
       740  -3304.5436      1007.8104     -4312.354       1292.54        0              953.21991      151384.85     -157942.97      511.0222       17105.347      225.55003      337.14459      1.9052777    
       760  -3343.3802      979.67539     -4323.0556      1321.1057      0              997.90912      151300.36     -157942.43      1427.7977      16926.678      219.25336      327.70326      1.9126072    
       780  -3352.1267      984.32591     -4336.4526      1345.4548      0              1015.3849      151245.23     -157942.52      1384.3652      16762.929      220.29416      329.2476       1.9501705    
       800  -3403.7211      972.99291     -4376.714       1363.3416      0              1024.0417      151180.2      -157944.29      1610.8468      16615.395      217.75781      325.3888       2.0560589    
       820  -3433.1225      1001.9316     -4435.0541      1372.3752      0              1009.7234      151126.85     -157944         963.30911      16483.47       224.23435      335.16413      1.9262344    
       840  -3471.2144      1009.2298     -4480.4441      1396.4686      0              1029.5813      151036.91     -157943.41      1550.2333      16364.19       225.86769      337.54243      2.0705223    
       860  -3496.0297      993.77161     -4489.8013      1421.809       0              1080.2247      150952.09     -157943.92      1768.4607      16258.518      222.40813      332.3833       2.0129583    
       880  -3524.9039      983.25681     -4508.1607      1428.2522      0              1085.716       150920.47     -157942.6       1496.1854      16168.46       220.05489      328.88725      1.9348561    
       900  -3554.976       957.40072     -4512.3767      1457.1352      0              1133.7234      150840.44     -157943.67      1879.8489      16092.777      214.26825      320.15601      2.0608864    
       920  -3602.0372      945.49243     -4547.5296      1481.0109      0              1124.8321      150790.02     -157943.39      1655.9603      16033.06       211.60315      316.21982      1.9425505    
       940  -3591.5561      974.67784     -4566.234       1476.5393      0              1124.3969      150777.31     -157944.48      1759.8207      15987.336      218.1349       325.97359      2.02081      
       960  -3623.7018      952.34885     -4576.0506      1486.4778      0              1135.9909      150747.1      -157945.62      1824.886       15954.657      213.13763      318.47226      2.041606     
       980  -3646.2301      931.78007     -4578.0101      1479.5377      0              1112.3231      150775.87     -157945.74      1185.7584      15935.247      208.53429      311.54728      2.0936951    
      1000  -3653.7611      983.29926     -4637.0604      1473.0616      0              1053.2459      150783.06     -157946.42      312.76781      15925.94       220.06439      328.87333      2.0051787    
      1020  -3689.0577      918.07231     -4607.13        1452.0618      0              1018.4708      150868.43     -157946.09      37.094231      15921.213      205.46647      307.05742      1.8736225    
      1040  -3709.5661      896.37545     -4605.9415      1412.9016      0              977.89877      150949.4      -157946.14     -439.08647      15917.777      200.61067      299.77073      1.8938039    
      1060  -3705.3479      933.08741     -4638.4353      1422.6668      0              973.20095      150910.68     -157944.98     -702.77283      15912.372      208.82688      312.0574       1.9481691    
      1080  -3738.2165      894.31115     -4632.5277      1440.029       0              1012.9439      150859.61     -157945.11     -82.790471      15903.297      200.14867      299.02843      1.9755193    
      1100  -3722.0599      886.69489     -4608.7548      1460.2634      0              1055.3838      150820.21     -157944.62      489.1459       15893.432      198.44414      296.52416      1.8743892    
      1120  -3737.9597      924.50073     -4662.4605      1487.5479      0              1072.2419      150722.9      -157945.15      329.11429      15886.677      206.90516      309.21675      1.8728731    
      1140  -3739.5122      939.25955     -4678.7718      1505.6179      0              1079.3128      150682.37     -157946.07      439.1228       15883.769      210.20822      314.06871      2.0673128    
      1160  -3763.5469      926.76507     -4690.3119      1481.5819      0              1039.3576      150732.29     -157943.54     -11.397313      15884.662      207.41193      309.90599      2.0230481    
      1180  -3740.6626      912.6751      -4653.3377      1459.7821      0              1038.313       150792.85     -157944.28      238.20475      15885.451      204.25856      305.2361       1.911067     
      1200  -3746.7725      930.06381     -4676.8363      1469.7494      0              1032.9215      150766.96     -157946.47     -219.76583      15885.359      208.15019      311.02813      1.9801669    
      1220  -3760.5728      881.49421     -4642.067       1432.3613      0              1008.0205      150863.96     -157946.41     -158.23995      15883.853      197.28021      294.80159      1.8424478    
      1240  -3750.3279      904.21967     -4654.5475      1458.3287      0              1018.2712      150814.74     -157945.88     -92.305609      15880.139      202.36622      302.33783      2.0194731    
      1260  -3780.485       887.6939      -4668.1789      1476.1019      0              1062.1361      150737.64     -157944.06      228.16384      15875.126      198.66772      296.81319      1.9712748    
      1280  -3784.1065      938.6391      -4722.7456      1509.6716      0              1061.8197      150651.68     -157945.92      1.2710199      15870.947      210.06936      313.89398      2.0101584    
      1300  -3817.2683      896.45206     -4713.7204      1491.8457      0              1057.5916      150683.48     -157946.64     -70.963075      15866.183      200.62781      299.73726      2.0076586    
      1320  -3814.7665      917.54153     -4732.308       1477.5528      0              1044.8205      150690.91     -157945.59     -343.05686      15861.169      205.34768      306.85934      1.9183121    
      1340  -3836.459       918.15601     -4754.615       1510.5303      0              1064.4321      150617.69     -157947.27     -121.61771      15854.493      205.4852       307.06354      1.9288968    
      1360  -3836.1321      907.0573      -4743.1894      1504.0599      0              1062.6279      150636.8      -157946.68     -174.21071      15846.403      203.00129      303.29045      2.0291277    
      1380  -3835.6816      907.24027     -4742.9219      1524.9974      0              1114.4381      150564.33     -157946.69      156.93744      15838.674      203.04224      303.36014      1.9984656    
      1400  -3828.7312      891.46129     -4720.1925      1526.9555      0              1116.2999      150582.21     -157945.66      708.75669      15834.027      199.51087      298.07923      1.9764829    
      1420  -3831.8386      900.64635     -4732.4849      1532.9689      0              1120.7559      150558.53     -157944.74      533.4961       15834.252      201.5665       301.17787      1.9210243    
      1440  -3806.1432      905.80909     -4711.9523      1523.0876      0              1104.2461      150606.49     -157945.78      549.94008      15838.424      202.72193      302.92751      1.9053317    
      1460  -3804.173       918.68515     -4722.8582      1490.6305      0              1068.9734      150663.84     -157946.3      -18.359522      15845.256      205.60362      307.21361      1.9781686    
      1480  -3827.9277      930.66555     -4758.5932      1501.6345      0              1066.4912      150619.73     -157946.45     -458.52159      15852.973      208.28486      311.23843      1.9539291    
      1500  -3819.9346      909.7601      -4729.6947      1498.9079      0              1055.6594      150662.1      -157946.36     -161.47046      15859.499      203.60618      304.21186      2.0072512    
      1520  -3841.7274      911.01234     -4752.7397      1532.4905      0              1095.9134      150564.88     -157946.02     -316.43863      15865.136      203.88643      304.62441      2.0150215    
      1540  -3864.153       900.50793     -4764.6609      1506.0503      0              1057.4393      150619.21     -157947.36     -601.44513      15870.12       201.53552      301.15289      1.895861     
      1560  -3863.0915      908.17147     -4771.263       1511.124       0              1025.2829      150638.33     -157946        -948.42744      15871.65       203.25064      303.73731      1.8735396    
      1580  -3865.9376      872.09827     -4738.0359      1510.6749      0              1047.8146      150651.14     -157947.67     -568.27304      15866.083      195.17738      291.70184      1.7445511    
      1600  -3844.7623      928.25703     -4773.0194      1511.1796      0              1037.5485      150625.04     -157946.79     -1053.187       15855.482      207.74583      310.52379      1.7822122    
      1620  -3836.9306      915.01367     -4751.9443      1505.8444      0              1061.1443      150627.46     -157946.39     -154.46401      15840.699      204.78194      306.04563      1.851316     
      1640  -3836.8514      924.75818     -4761.6096      1524.9851      0              1059.85        150598.87     -157945.32     -523.89939      15823.41       206.96278      309.28712      1.9027922    
      1660  -3862.4415      912.89422     -4775.3358      1512.1293      0              1034.1678      150622.88     -157944.51     -1012.2065      15802.47       204.3076       305.32214      1.8700028    
      1680  -3852.4384      912.10922     -4764.5476      1519.1972      0              1071.6496      150590.76     -157946.15      99.390736      15776.532      204.13191      305.0342       1.9261295    
      1700  -3857.9441      910.09304     -4768.0372      1518.0412      0              1089.3203      150571.18     -157946.58      87.303447      15748.941      203.68069      304.36415      1.9135939    
      1720  -3867.273       908.61014     -4775.8832      1536.3611      0              1134.1892      150500.11     -157946.54      275.558        15722.317      203.34882      303.88087      1.8825688    
      1740  -3887.1112      906.61042     -4793.7216      1549.0779      0              1126.8223      150474.69     -157944.31      235.52142      15698.228      202.90127      303.18296      1.9424675    
      1760  -3866.123       884.06964     -4750.1927      1525.7978      0              1114.0504      150555.93     -157945.97      778.81889      15675.346      197.8566       295.677        1.8171558    
      1780  -3870.6981      918.24644     -4788.9445      1549.7654      0              1092.7163      150515.18     -157946.61     -279.77719      15655.57       205.50544      306.97435      2.1558812    
      1800  -3854.9761      895.11874     -4750.0948      1540.0963      0              1117.2238      150537.9      -157945.32      618.59881      15635.605      200.32941      299.35093      1.8800504    
      1820  -3873.8476      887.22378     -4761.0714      1534.1073      0              1108.1968      150543.57     -157946.94      661.13525      15617.005      198.5625       296.63847      2.0163819    
      1840  -3897.846       903.11583     -4800.9619      1511.2621      0              1042.6798      150590.92     -157945.82     -671.92064      15599.083      202.11918      302.04557      1.8836564    
      1860  -3906.3415      893.64493     -4799.9864      1533.4366      0              1048.3334      150563.71     -157945.47     -798.699        15577.351      199.99957      298.76788      2.0574418    
      1880  -3909.0563      876.43443     -4785.4908      1533.9702      0              1096.3891      150528.27     -157944.12      298.08795      15551.652      196.14782      293.03935      1.9771518    
      1900  -3909.8566      875.01718     -4784.8738      1548.3287      0              1109.3356      150503.11     -157945.65      202.88108      15526.5        195.83064      292.54591      2.0159556    
      1920  -3922.4726      871.87865     -4794.3512      1576.5497      0              1148.624       150427.11     -157946.64      670.0381       15502.758      195.12823      291.5128       1.9779752    
      1940  -3931.983       907.49782     -4839.4808      1567.5666      0              1109.7913      150428.03     -157944.87     -413.00248      15482.417      203.09987      303.49293      1.9110289    
      1960  -3962.1377      869.05061     -4831.1884      1572.3178      0              1081.2427      150459.82     -157944.57     -282.75444      15462.582      194.49531      290.5705       1.9480205    
      1980  -3937.7887      882.77852     -4820.5672      1555.4522      0              1111.9478      150458.82     -157946.79      234.39924      15441.065      197.56764      295.1511       2.0059252    
      2000  -3939.8307      896.54164     -4836.3724      1607.3286      0              1150.4669      150352.85     -157947.01      671.82238      15419.984      200.64786      299.85583      1.8357328    
Loop time of 15.7823 on 4 procs for 2000 steps with 2500 atoms

Performance: 10.949 ns/day, 2.192 hours/ns, 126.724 timesteps/s, 316.811 katom-step/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 8.9497     | 9.3035     | 9.5988     |   9.5 | 58.95
Bond    | 0.0041718  | 0.0044795  | 0.0047093  |   0.3 |  0.03
Kspace  | 1.8786     | 2.5408     | 3.1035     |  33.3 | 16.10
Neigh   | 0.94163    | 1.0429     | 1.1386     |   9.4 |  6.61
Comm    | 1.1122     | 1.3806     | 1.7855     |  22.6 |  8.75
Output  | 0.0027737  | 0.0030493  | 0.0038583  |   0.8 |  0.02
Modify  | 1.3762     | 1.4793     | 1.5979     |   7.9 |  9.37
Other   |            | 0.0276     |            |       |  0.17

Nlocal:            625 ave         630 max         616 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost:        13474.8 ave       13631 max       13322 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         582237 ave      616081 max      544712 min
Histogram: 1 0 0 1 0 0 0 1 0 1

Total # of neighbors = 2328949
Ave neighs/atom = 931.5796
Ave special neighs/atom = 4
Neighbor list builds = 102
Dangerous builds = 0

Total wall time: 0:00:15
